Tom Stahl of A History of Violence used to be a very nasty mobster, until he'd had enough and remade his personality, made up a fake history, and became a Nice Guy restaurant owner in a small town. The film opens with him being perfectly willing to let some gunmen rob his store's money until they implied they'd shoot them all anyway... then he brutally disarmed them.
Oz of The Whole Nine Yards. So much so that the person his wife hired to kill him couldn't bring herself to do it and became his assistant instead. This saves his life again in the end of the movie when Jimmy kills his partner to avoid having to kill Oz.
Kurtis in The Final. He tried his best to be friends to everybody, and defended Ravi from Bradley. As a result, the outcasts try (and fail) to keep him from coming to their "party."
Dale, one of the unfortunate victims in Horrible Bosses, claims that his childhood dream was to become a husband. He's a very mild-mannered guy who spends most of the film in over his head, though every once in a while he snaps.
Several of Jim Carrey's characters fall into this category.
Stanley Ipkiss in The Mask is specifically identified as a 'nice guy' - unfortunately for him that means being treated like a doormat. Then comes the Mask...
Truman Burbank in The Truman Show. This is the particular reason the show is centered around him and you genuinely feel sorry for the guy watching him discover that the only world he ever knew is nothing but a sham devised by a scheming TV producer.
Charlie Baileygates in Me, Myself & Irene. Again, that means to be treated like an Extreme Doormat: after his wife cheats on him for a midget and leaves behind three illegitimate sons, Charlie lets everybody step on him like dirt, refusing to accept this. Over time, something begins to borrow up inside of him and creates an alter ego named Hank that unleashes the years of pent-up anger.
Professor X opens his heart and his home to mutants who feel persecuted by the outside world.
Logan: There's not many people that will understand what you're going through, but I think this guy Xavier is one of them. He seems to genuinely want to help you, and that's a rare thing for people like us.
Captain America. When asked if he wants to kill Nazis: "I don't want to kill anyone. I don't like bullies. I don't care where they're from". 100% honesty.
Julio from Elysium. Although he's a car thief, he's never shown to be anything but friendly and an unfailingly loyal friend to Max.
The title character of Carrienote Technically a novel first, but the film adaptations make this especially evident is one of these: She loves her mother dearly, despite the latter's horribly abusive behavior towards her and when her English class is asked for criticisms of a fellow student's poem, she raises her hand and expresses heartfelt admiration for it when called on. Unfortunately for those who tormented her, she is also a fine example of why you should Beware the Nice Ones.
The title characters from Tucker & Dale Vs. Evil (especially Dale) are so well-meaning and friendly you can't help but feel bad for them as their vacation falls apart.
Ford Brody from Godzilla (2014), is a loving father and a spouse and very patient with his more-than-a-little crazy dad. The moment he hears Joe has been arrested in Japan he rushes to his side and tries to convince him to come home with him.